• HclsigDscussionTopics

Vision: Bench to Bedside

This is a collection of topics and references to those topics that are proposed by the intended participants of the first F2F meeting of the HCLSIG group. It aims to better prepare the participants for the break-out session discussions.

The following table is subjected to change according to the email responses from the HCLSIG Members.

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  Topics ||Description ||Interested Participants ||References ||

  Ontologies and Knowledge Presentation
  bioMedical ontologies		Mark Musen	The National Center for Biomedical Ontology
  Collaborative Ontology Development	Terminological Federation, Group Communication Structures, Social Networks, Meaning Negotiation, Consensus Derivation, Web of Trust, Peer Review, Wikis	Mark Musen, John Madden, Eric Neumann, Vipul Kashyap, Marja-Riitta Koivunen, Vinay Chaudhri, Pat Croke, Alfredo Morales	Annotea social bookmarks and topics?
  scientific literature	semantics and literature - including semantics of authorship (FOAF?)	Matt Cockerill
  	aggregation of scientific literature	Jon Wilbanks, Michael Schroeder, Marja-Riitta Koivunen, Vinay Chaudhri
  	Knowledge Ecosystems	Tim Clark
  semantic annotation of unstructured data		Davide Zaccagnini, John Madden, Alfredo Morales
  Workflow and Pathways
  BioPAX pathway knowledge	BioPAX is a collaborative effort to create a data exchange standard for biological pathway data. It is written in OWL. | Luciano_BioPAX	Joanne Luciano, Eric Neumann	www.biopaxwiki.org
  Protocolization	Knowledge Merging and Specification, Clinical Process Specification, Intentions, Actions, Outcomes	Tonya Hongsermeier, Sam Brandt, Helen Chen, Vipul Kashyap, Alfredo Morales, Davide Zaccagnini	Adaptive Clinical Protocols and Pathways Subgroup

  Knowledge Management for Decision Support
  knowledge management	semantic models for clinical knowledge e.g., rules, templates, guidelines, etc., use of semantic technologies for knowledge maintenance and update, dependency propagation, provenance	Tonya Hongsermeier, Vipul Kashyap, Alfredo Morales, Eric Neumann, Marja-Riitta Koivunen, Davide Zaccagnini, Helen Chen
  Aggregation of Structured Data
  bioinformatic databases	data types and intrinsic semantics, unique identifiers, LSID and metadata	Eric Neumann	UniProt rdf
  data from OMICS experiments	gene expression, metabolomics, in vitro studies, preclinical and clinical biomarkers	Eric Neumann
  Making semantic webs work
  Issue 1: naming	How to overcome age-old problems with naming, synonyms, homonyms, hyponyms etc.	Robert Stevens, Alfredo Morales
  Issue 2: annotation / mapping	Mechanisms for annotating large data sets, mapping data into ontologies	Robert Stevens, Marja-Riitta Koivunen, Davide Zaccagnini
  Semantic Web Services	Annotating registries of Web Services with biomedical ontologies. Making services easier to find and interoperate	Duncan Hull, Alfredo Morales	BioMOBY, Taverna, OWL-S and the Web Service Modelling Ontology (WSMO)